dom.rb in mspire-0.4.2

- old
+ new

@@ -1,107 +1,132 @@
 require 'xml_style_parser'
 require 'ms/spectrum'
 require 'ms/scan'
+require 'ms/parser/mzxml'
+require 'tempfile'
 
 
 class MS::Parser::MzXML::DOM
   include XMLStyleParser
   include MS::Parser::MzXML
 
-  #@@scan_atts = %w(num msLevel retentionTime startMz endMz precursors spectrum)
+  NetworkOrder = true
 
+  #@@scan_atts = %w(num msLevel retentionTime startMz endMz precursor spectrum)
+
   def initialize(parse_type=:msrun, version='1.0')
     @method = parse_type
     @version = version
   end
 
   def new_scan_from_hash(node)
     scan = MS::Scan.new  # array class creates one with 9 positions
     scan[0] = node['num'].to_i
     scan[1] = node['msLevel'].to_i
-    scan[2] = node['retentionTime'][2...-1].to_f
+    if x = node['retentionTime']
+      scan[2] = x[2...-1].to_f
+    end
     if x = node['startMz']
       scan[3] = x.to_f
       scan[4] = node['endMz'].to_f
     end
     scan
   end
 
+  # assumes that node contains scans and checks any scan nodes for children
+  def add_scan_nodes(nodes, scans, scn_index, scans_by_num, lazy, io)
+    nodes.each do |scan_n|
+      scan = create_scan(scan_n, scans_by_num, lazy, io)
+      scans[scn_index] = scan
+      scans_by_num[scan[0]] = scan 
+      scn_index += 1
+      if @version > '1.0'
+        new_nodes = scan_n.find('child::scan')
+        if new_nodes.size > 0
+          scn_index = add_scan_nodes(new_nodes, scans, scn_index, scans_by_num, lazy, io)
+        end
+      end
+    end
+    scn_index
+  end
+
   # takes a scan node and creates a scan object
   # the parent scan is the one directly above it in mslevel
-  # if the 
-  def create_scan(scan_n, scans_by_num, get_spectra=true)
-    if @version < '3.0'
-      scan = new_scan_from_hash(scan_n)
-      precs = []
-      scan_n.each do |node|
-        case node.name
-        when 'precursorMz'
-          # should be able to do this!!!
-          #scan[5] = scan_n.find('child::precursorMz').map do |prec_n|
-          prec = MS::Precursor.new
-          prec[1] = node['precursorIntensity'].to_f
-          prec[0] = node.content.to_f
-          if x = node['precursorScanNum']
-            prec[2] = scans_by_num[x.to_i]
-          end
-          precs << prec
-        when 'peaks'
-          next unless get_spectra
+  # lazy must be a symbol from MS::MSRun.new
+  def create_scan(scan_n, scans_by_num, lazy, io=nil)
+    scan = new_scan_from_hash(scan_n)
+    prec = nil
+    scan_n.each do |node|
+      case node.name
+      when 'precursorMz'
+        # should be able to do this!!!
+        #scan[5] = scan_n.find('child::precursorMz').map do |prec_n|
+        raise RuntimeError, "the msrun object can only handle one precursor!" unless prec.nil?
+        prec = MS::Precursor.new
+        prec[1] = node['precursorIntensity'].to_f
+        prec[0] = node.content.to_f
+        if x = node['precursorScanNum']
+          prec[2] = scans_by_num[x.to_i]
+        end
+      when 'peaks'
+        case lazy
+        when :no_spectra
+          next
+        when :string
+          scan[6] = MS::Spectrum::LazyString.from_base64_peaks(node.content, node['precision'].to_i)
+        when :io
+          # assumes that parsing was done with a LazyPeaks parser!
+          nc = node.content
+          scan[6] = MS::Spectrum::LazyIO.new(io, nc.first, nc.last, node['precision'].to_i, MS::Parser::MzXML::DOM::NetworkOrder)
+        when :not
           # SHOULD be able to do this!!
           #peaks_n = scan_n.find_first('child::peaks')
           scan[6] = MS::Spectrum.from_base64_peaks(node.content, node['precision'].to_i)
         end
       end
-      scan[5] = precs
-      scan
-    else  # for version > 3.0 
-      abort 'not supporting version 3.0 just yet'
-      # note that mzXML version 3.0 *can* have more than one peak...
-      # I'm not sure how to deal with that since I have one spectrum/scan
     end
+    scan[5] = prec
+    scan
   end
 
 
   # returns an array of msrun objects
   def msruns(file)
     raise NotImplementedError
   end
 
-  # returns a string with double </scan></scan> tags into single and missing
-  # </scan> tags after peaks added in
-  # we do this in windows style since these are generated off a windows
-  # machine only
-  def fix_bad_scan_tags(file)
-    IO.read(file).gsub(/<\/scan>\s+<\/scan>/m, '</scan>').gsub(/<\/peaks>\s+<scan/m, "</peaks>\r\n  </scan>\r\n  <scan")
-  end
-
-  # right now cannot parse multiple runs out of an mzXML version 2 file since
+    # right now cannot parse multiple runs out of an mzXML version 2 file since
   # this is built around a single run per file
   # OPTIONS:
-  #   :msrun => MSRun    # use this object instead of creating one
-  #   :spectra => *true|false   # if false don't get spectra
+  #   :msrun => (an MSRun object)   # use this object instead of creating one
+  #   :lazy => [See MS::MSRun for documentation]
   def msrun(file, opts={})
-    unless opts.key?(:spectra)
-      opts[:spectra] = true
-    end
+    #unless opts.key?(:spectra)
+    #  opts[:spectra] = true
+    #end
 
     msrun_obj = 
       if x = opts[:msrun]
         msrun_obj = x
       else
         MS::MSRun.new
       end
 
-    root = 
-      if @version == '2.0'
-        string = fix_bad_scan_tags(file)
-        get_root_node_from_string(string)
+    io =
+      if file.is_a? String  # a filename
+        filename = file
+        File.open(file) 
       else
-        get_root_node_from_file(file)
+        file
       end
 
+    root = get_root_node_from_io(io)
+
+    if filename
+      io.close  # can close now
+    end
+
     # right now we are only finding the first msRun (probably a rare case of
     # multiple runs in an mzXML file...)
     msrun_n = 
       if @version >= '2.0' 
         kids = root.children.select {|v| v.name == 'msRun' }
@@ -116,30 +141,29 @@
 
     ## HEADER
     scan_count = msrun_n['scanCount'].to_i
     msrun_obj.scan_count = scan_count
     scans_by_num = Array.new(scan_count + 1)
-    
+
     ## SPECTRUM
     parent = nil
     scans = Array.new( scan_count )
     scn_index = 0
 
     # we should be able to do this, but it's not working!!!
     #scan_n = msrun_n.find_first('scan')
     #while (scn_index < scan_count)
-    get_spectra = opts[:spectra]
+    lazy = opts[:lazy]
 
-    msrun_n.each do |scan_n|
-      next unless scan_n.name == 'scan'
-      scan = create_scan(scan_n, scans_by_num, get_spectra)
-      scans[scn_index] = scan
-      #sc = scan_n.next
-      scans_by_num[scan[0]] = scan 
-      scn_index += 1
+    if @version >= '3.0'
+      warn '[version 3.0 parsing may fail if > 1 peak list per scan]'
+      # note that mzXML version 3.0 *can* have more than one peak...
+      # I'm not sure how to deal with that since I have one spectrum/scan
     end
 
+    scan_nodes = msrun_n.find('child::scan')
+    add_scan_nodes(scan_nodes, scans, scn_index, scans_by_num, lazy, io)
 
     ## update the scan's parents
     MS::MSRun.add_parent_scan(scans)
 
     # note that startTime and endTime are optional AND in >2.2 are dateTime
@@ -149,11 +173,10 @@
     # really minutes.  All the more reason to use the first and last scans!
     msrun_obj.start_time = scans.first.time
     msrun_obj.end_time = scans.last.time
 
     msrun_obj.scans = scans
-  end
 
+  end
 end
-
 
 